Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes

The refined crystal structures of HhaI methyltransferase complexed with cognate unmethylated or methylated DNA together with S-adenosyl-L-homocysteine, along with the previously-solved binary and covalent ternary structures, offer a detailed picture of the active site at individual stages throughout the reaction cycle. This picture supports and extends a proposed mechanism for C5-cytosine methylation that may be general for the whole family of C5-cytosine methyltransferases. The structures of the two new complexes have been refined to crystallographic R-factors of 0.189 and 0.178, respectively, at 2.7 A resolution. We observe that both unmethylated 2'-deoxycytidine and 5-methyl-2'-deoxycytidine flip out of the DNA helix and fit into the active site of the enzyme. The catalytic sulfur atom of Cys81 interacts strongly with C6. The C5 methyl group of the flipped 5-methyl-2'-deoxycytidine is bent approximately 50 degrees out of the plane of the cytosine ring and towards the sulfur atom of S-adenosyl-L-homocysteine. This unusual position is probably due to partial sp3 character at C5 and C6 and to steric effects of the conserved amino acid residues Pro80 and Cys81. Two water molecules are held near the hydrophobic edge (C5 and C6) of the flipped cytosine by two conserved amino acid residues (Gln82 and Asn304) and the phosphoryl oxygen atom of the phosphate group 3' to the flipped nucleotide, and one of them may serve as the general base for eliminating the proton from C5. Protonation of the cytosine N3 during the methylation reaction may involve Glu119, which itself might be protonated via a water-mediated interaction between the terminal carboxyl group of Glu119 and the amino group of the methionine moiety of S-adenosyl-L-methionine. The cofactor thus plays two key roles in the reaction.

Charge-state reduction with improved signal intensity of oligonucleotides in electrospray ionization mass spectrometry

The shift of charge states of oligonucleotide negative ions formed in electrospray ionization mass spectrometry to higher mass-to-charge ratio has been accomplished by addition of organic acids and bases to the solution to be electrosprayed. The use of acetic acid or formic acid combined with piperidine and imidazole effectively reduced charge states. Signal intensity and stability were enhanced greatly when the infused solution contained a high percentage of acetonitrile. In addition, the cocktail that contained imidazole, piperidine, and acetic acid in 80% acetonitrile not only reduced charge states, but also substantially suppressed Na adduction. Several oligonucleotides that varied in base composition and length were investigated, and studies of mixtures showed a significant reduction in spectral complexity.

Characterization of the murine antibody response to peptides representing the variable domains of the major outer membrane protein of Chlamydia pneumoniae

In an attempt to gain more knowledge about the immunogenicity of the variable domains (VDs) of the major outer membrane protein (MOMP) of Chlamydia pneumoniae, peptides representing these areas were used to immunize BALB/c and C57BL/6 mice. Antisera to the peptides and to peptides conjugated to keyhole limpet hemocyanin (KLH) were characterized by their ability to recognize the immunizing peptide and elementary bodies (EBs) of C. pneumoniae by enzyme-linked immunosorbent assay (ELISA) and Western blot (immunoblot). In addition, antiserum was analyzed for its molecular specificity by a pepscan as well as its in vitro neutralizing ability. In general, results obtained with antisera to the peptides paralleled the results obtained with the antisera to the KLH-conjugated peptides except that the titers or strength of reaction in the assays was less. Antisera to the VDs in both strains of mice gave ELISA titers to the homologous VD peptide ranging from 1,000 to >64,000. The strength of reactivity with the reduced MOMP as judged by Western blot, in most cases, paralleled the ELISA titer to the peptide. However, only antisera raised in both strains of mice to the VD1 and VD4 peptides reacted strongly with the EBs, suggesting surface exposure of these VDs. In addition, antisera to VD3 from C57BL/6 mice gave strong reactivity to EBs. By pepscan analysis antisera from both strains of mice reacted with several VD1 and VD3 octameric peptides, with weaker reactivity being seen with the octameric peptides in the other two VDs. This was in contrast to antisera raised to EBs of C. pneumoniae TW-183, which identified two immunogenic regions, one in VD1 and the other mapped to VD4. While antisera raised to EBs strongly neutralized the infectivity of C. pneumoniae, none of the peptide antisera was able to neutralize. In addition, peptides to the VDs were not able to block the neutralizing ability of the antisera to EBs of C. pneumoniae. Therefore, these results suggest that the VDs of the MOMP of C. pneumoniae are surface exposed but do not elicit neutralizing antibodies when linear peptides representing them are used as the immunogen.

Mass spectrometric characterization of sequence-specific complexes of DNA and transcription factor PU.1 DNA binding domain

Electrospray ionization mass spectrometry (ESI-MS) has been used to study the noncovalent interaction of the 13.5-kDa DNA binding domain of PU.1 (PU.1-DBD) with specific double-stranded DNA (dsDNA) target molecules. Mixtures of PU.1-DBD protein and wild-type target DNA sequence yielded ESI-MS spectra showing only protein-dsDNA complex ions of 1:1 stoichiometry and free dsDNA. When PU.1-DBD protein, wild type target DNA, and a mutant target DNA lacking the consensus sequence were mixed, only the 1:1 complex with the wild-type DNA was observed, consistent with gel electrophoresis mobility shift assay results, demonstrating the observation of sequence-specific protein-dsDNA complexes using ESI-MS.

Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry

The binding stoichiometry of gene V protein from bacteriophage f1 to several oligonucleotides was studied using electrospray ionization-mass spectrometry (ESI-MS). Using mild mass spectrometer interface conditions that preserve noncovalent associations in solution, gene V protein was observed as dimer ions from a 10 mM NH4OAc solution. Addition of oligonucleotides resulted in formation of protein-oligonucleotide complexes with stoichiometry of approximately four nucleotides (nt) per protein monomer. A 16-mer oligonucleotide gave predominantly a 4:1 (protein monomer: oligonucleotide) complex while oligonucleotides shorter than 15 nt showed stoichiometries of 2:1. Stoichiometries and relative binding constants for a mixture of oligonucleotides were readily measured using mass spectrometry. The binding stoichiometry of the protein with the 16-mer oligonucleotide was measured independently using size-exclusion chromatography and the results were consistent with the mass spectrometric data. These results demonstrate, for the first time, the observation and stoichiometric measurement of protein-oligonucleotide complexes using ESI-MS. The sensitivity and high resolution of ESI-MS should make it a useful too] in the study of protein-DNA interactions.

[Simultaneous rhinoplasty and blepharoplasty]

Simultaneous rhinoplasty and blepharoplasty are the commonest facial cosmetic operation. The paper presents 73 cases who underwent this procedure with satisfactory results from Jan. 1989 to Nov. 1993. The authors described operation steps, e.g., making lacuna in the dorsum, lengthening nasal columella, nasal tip plasty. It was emphasized that the pretarsal flap should contain complete network of the superficial fascia, and the soft tissue underneath be trimmed. All the dissection should be kept in the same cleavage, which would reduce intraoperative bleeding and postoperative edema.

[An experimental study of tumor necrosis factor (TNF) and interleukin-1 (IL-1) in aqueous humor after intraocular lens implantation]

OBJECTIVE

The tumor necrosis factor (TNF) and interleukin-1 (IL-1) levels in aqueous humor after intraocular lens (IOL) implantation were studied in rabbit eyes and their effects on post-operative anterior ocular inflammation were discussed.

METHODS

27 adult pigmented rabbits were divided into three groups: (1) Lens extraction and intraocular lens (IOL) implantation in the capsular bag. (2) Simple extracapsular lens extraction, and (3) normal control group without surgical intervention. Aqueous humor samples were aspirated on days 1, 3, 7 and 14 postoperatively. A modified double-antibody indirect sandwich ELISA was used to detect for the presence of TNF. MTT colorimetry was used to detect for the presence of IL-1. The data were analysed statistically.

RESULTS

TNF and IL-1 levels in the aqueous humor were significantly higher (P < 0.05) at 1, 3, 7, and 14 days postoperatively in IOL implanted group than that in the control group, and TNF levels in aqueous humor at 3, 7 and 14 days postoperatively and IL-1 levels at 1 and 3 days postoperatively were significantly higher (P < 0.05) in IOL implanted group than that in simple extracapsular lens extraction group (P < 0.05). In the postoperative 7-14 days, the TNF and in the 3 to 14 days the IL-1 in the aqueous humor reached their maximum levels in IOL implantation group.

CONCLUSIONS

It is reasonable to consider that the increases of TNF and IL-1 levels may play critical roles in the anterior ocular inflammation response after IOL implantation.

Reversal by L- and D-enantiomers of NG-nitro-arginine of endotoxin-induced hypotension and vascular hyporesponsiveness

We examined the effects of D-NNA (NG-nitro-D-arginine) and L-NNA (NG-nitro-L-arginine) on suppression of Escherichia coli lipopolysaccharide (LPS)-induced vascular hyporeactivity in pentobarbital-anesthetized rats. Mean arterial pressure (MAP) and pressor response to norepinephrine (NE) were reduced at 40 min (early phase) and 3.5-4 h (late phase) after i.v. injection of LPS (10 mg/kg). Pretreatment with either D-NNA (16 mg/kg) or L-NNA (8 mg/kg) abolished LPS-induced reduction in MAP and hyporesponsiveness to NE during the early phase but not the late phase of endotoxemia and increased mortality. In contrast, posttreatment with D-NNA and L-NNA at 3 h after the injection of LPS prevented further decreases of MAP and pressor response to NE during the late phase of endotoxemia. The restoration of vascular response by pretreatment with either D-NNA or L-NNA during the early phases or posttreatment with either of these two agents during the late phase of endotoxemia was abolished by i.v. infusion (10 mg/kg/min) of L-arginine (L-Arg), but not D-arginine (D-Arg), suggesting involvement of the L-Arg/ nitric oxide pathway.

Structural basis for selectivity of the isoquinoline sulfonamide family of protein kinase inhibitors

A large family of isoquinoline sulfonamide compounds inhibits protein kinases by competing with adenosine triphosphates(ATP), yet interferes little with the activity of other ATP-using enzymes such as ATPases and adenylate cyclases. One such compound, N-(2-aminoethyl)-5-chloroisoquinoline-8-sulfonamide (CK17), is selective for casein kinase-1 isolated from a variety of sources. Here we report the crystal structure of the catalytic domain of Schizosaccharomyces pombe casein kinase-1 complexed with CK17, refined to a crystallographic R-factor of 17.8% at 2.5 angstrom resolution. The structure provides new insights into the mechanism of the ATP-competing inhibition and the origin of their selectivity toward different protein kinases. Selectivity for protein kinases versus other enzymes is achieved by hydrophobic contacts and the hydrogen bond with isoquinoline ring. We propose that the hydrogen bond involving the ring nitrogen-2 atom of the isoquinoline must be preserved, but that the ring can flip depending on the chemical substituents at ring positions 5 and 8. Selectivity for individual members of the protein kinase family is achieved primarily by interactions with these substituents.

Finding a basis for flipping bases

Rotation of a DNA nucleotide out of the double helix and into a protein binding pocket ('base flipping') was first observed in the structure of a DNA methyltransferase. There is now evidence that a variety of proteins use base flipping in their interactions with DNA. Though the mechanism for base flipping is still unclear, we propose a three-step pathway: recognizing the target site and increasing the interstrand phosphate-phosphate distance nearby, initiating base flipping by protein invasion of the DNA, and trapping the flipped DNA structure.

Specific metal-oligonucleotide binding studied by high resolution tandem mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) was used to study the binding of metal ions to two oligonucleotides, d(pGCTTGCATp) and d(TTGGCCCTCCTT). Collision-induced dissociation (CID) of the metal-oligonucleotide complex revealed that metal ions preferentially bound to the central thymine region of the sequence. The most probable binding sites were the phosphodiester backbone since the sum of the maximum number of charge addition from the metal ions and the charge state of the whole complex was found to be equal to the number of ionizable protons on the DNA backbone. Although site-specific and sequence-specific binding was observed for all three of the metal ions studied, the binding specificity of UO2(2+) ions was significantly greater than for Mg2+ and Na+. These experiments demonstrate that ESI-MS/MS can be applied to study the binding of metal ions and their complexes to oligonucleotides, providing not only information on the number of metal ions binding to the oligonucleotide, but also information related to the binding site(s) and binding specificity.

Molecular weight determination of plasmid DNA using electrospray ionization mass spectrometry

Ionization and molecular weight (MW) determination of megadalton size plasmid DNA has been achieved using electrospray ionization (ESI) with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. DNA molecules were shown to remain intact through electrospray ionization by collection on a specially prepared surface, followed by agarose gel electrophoresis. Individual highly charged ions of plasmid DNA produced by ESI were trapped in an FTICR cell for up to several hours and reacted with acetic acid to induce charge state shifts. Measurements of mass-to-charge ratios for these multiple peaks arising from charge state shifting give MW measurements of individual ions with an average accuracy of 0.2%. The MW distribution was obtained by measurements for a number of individual ions from the same sample [plasmid DNA: pGEM-5S MW(cal) = 1.946 MDa], yielding a MW(obs) of 1.95 +/- 0.07 MDa for ions clustered in the vicinity of the expected MW.

Identification of a biologically significant DNA-binding peptide motif by use of a random phage display library

A peptide library approach was used to identify peptides that could bind to different DNA structures. A 23-mer random peptide library was displayed in the context of the pIII protein of M13 filamentous phage. Double-stranded (ds) oligodeoxyribonucleotides (oligos) were immobilized in 96-well plates using either chemical conjugation or a biotin-avidin linking method. Individual phage clones capable of binding to immobilized oligos were selected from the phage library. Using a plaque dilution assay for rapid screening of binding preferences, four groups of oligo-binding (OB) phage were tentatively identified as showing preference for: (1) single-stranded (ss) oligos irrespective of sequence; (2) ds oligos irrespective of sequence; (3) sequence-specific binding to ss oligos; and (4) weak non-specific binding to all types of oligos tested. A quantitative solution-phase competition assay was used to confirm the ability of certain phage to discriminate ss from ds oligos. A consensus motif, FGRA, was found in those phage clones that preferentially bound ss oligos; this motif has previously been noted in the binding domains of several ribonucleoproteins and ss DNA-binding proteins. Peptides based on the FGRA motif, but not scrambled controls, were able to inhibit the binding of appropriate phage clones or of Escherichia coli ss DNA-binding protein to oligos. This suggests that amino acid sequences that are capable of affecting biologically significant protein-DNA interactions can be identified from random peptide libraries using phage display techniques.

Screening derivatized peptide libraries for tight binding inhibitors to carbonic anhydrase II by electrospray ionization-mass spectrometry

This paper describes the use of electrospray ionization-mass spectrometry (ESI-MS) to screen two libraries of soluble compounds to search for tight binding inhibitors for carbonic anhydrase II (EC 4.2.1.1). The two libraries, H2NO2SC6H4C(O)NH-AA1-AA2-C(O)NHCH2CH2CO2H where AA1 and AA2 are L-amino acids (library size: 289 compounds) or D-amino acids (256 compounds), were constructed by attaching tripeptides to the carboxyl group of 4-carboxybenzenesulfonamide. Screening of both libraries yielded, as the tightest binding inhibitor, compound 1 (AA1 = AA2 = L-Leu; binding constant Kb = 1.4 x 10(8) M-1). The ability of ESI-MS to estimate simultaneously the relative binding affinities of a protein to soluble ligands in a library, if general, should be useful in drug development.

Construction and rapid testing of synthetic and modified toxin gene sequences CryIA (b&c) by expression in maize endosperm culture

The synthesis of two modified genes, Cry IA(b) and CryIA(c), each consisting of 1845 bp, is described in detail. The genes were synthesized using an improved PCR procedure based on recursive principles. The synthetic CryIA(c) gene was put under the control of a maize ubiquitin promoter. This construct was tested in a maize endosperm-derived suspension culture system. The use of maize endosperm culture as a quick and efficient system to test the activity of synthetic genes is described.

Ionizing radiation-induced phosphorylation of RPA p34 is deficient in ataxia telangiectasia and reduced in aged normal fibroblasts

Replication protein A (RPA, also called human single stranded DNA binding protein, hSSB) is a trimeric, multifunctional protein complex involved in DNA replication, DNA repair and recombination. Phosphorylation of RPA p34 subunit is observed after exposure of cells to radiation and other DNA damaging agents, which implicates the protein not only in repair but also in the regulation of replication on damaged DNA template. Here, we show that the phosphorylation observed in RPA p34 after exposure to ionizing radiation, X- or gamma-rays, is reduced and occurs later in primary fibroblasts from patients suffering from ataxia telangiectasia (AT), as compared to normal fibroblasts. We also show that in primary normal human fibroblasts, radiation-induced phosphorylation of RPA p34 is 'age'-dependent and decreases significantly as cultures senesce. Radiation-induced phosphorylation of RPA p34 is nearly absent in non-cycling cells, while the expression of p21cipl/wafl/sdil remains inducible. The results demonstrate a growth-state and culture-age dependency in radiation-induced RPA p34 phosphorylation, and suggest the operation of a signal transduction pathway that is inactivated in senescing or quiescent fibroblasts and defective in AT cells.

Effects of conserved residues on the regulation of rabbit muscle pyruvate kinase

A cDNA encoding the complete rabbit muscle pyruvate kinase isozyme (RMPK) was cloned using the method of rapid amplification of cDNA ends. The sequence encodes a polypeptide chain of 530 amino acids which differs in three amino acid residues from a sequence reported by Larsen et al. (Larsen, T.M., Laughlin, T., Holden, H.M., Rayment, L, and Reed, G.H. (1994) Biochemistry 33, 6301-6309). Glu233-Gln234 and Ala400 were identified instead of Asp233-Glu234 and Ser400, respectively. The recombinant RMPK was overexpressed in the Escherichia coli JM 105 cells. Purified recombinant pyruvate kinase displayed identical physical and enzymatic properties as the authentic enzyme. Three point mutants of RMPK were constructed using site-directed mutagenesis. Like the wild type RMPK, sedimentation, and CD spectroscopic studies show that purified RI 19C and T340M are tetrameric proteins with similar secondary and tertiary structures. Mutant R119C enzyme exhibits 0.6% of the value of k(cat) and an order of magnitude decrease in the apparent affinity for ADP as compared to the wild type PK. The overall response to inhibitor and activator, Phe and FBP, respectively, were not affected by the R119C mutation. The T340M mutant enzyme is only half as active as the wild type PK. T340M is more susceptible to inhibition by Phe but apparently is not responsive to the activator FBP. The kinetic behavior of the Q377K mutant enzyme is in between that of the R119C and T340M mutants exhibiting 5% of the wild type enzymatic activity and an enhanced sensitivity to the inhibitor, Phe, while maintaining the same responsiveness to FBP and apparent affinities for substrates. The significant decrease in activity in all three mutants mimics the exact consequences of the same mutations in human erythrocyte PK from hemolytic anemia patients. Thus, this study demonstrates not only the effects of these conserved residues in the regulatory properties of mammalian PK. but also that the observed effects are most likely applicable to all isozymic forms of PK.

The effect of orientation within a chimeric peptide on the immunogenicity of Chlamydia trachomatis epitopes

Peptides representing the Chlamydia trachomatis major outer membrane protein variable domains (VD) 1 and 4 of serovars C and E, respectively, have been shown to elicit a neutralizing antibody response in mice. To assess whether the position within a chimeric peptide influences the immunogenicity of the epitopes, two constructs, VD 1-4 and VD 4-1, were made in which the position of the VD relative to the amino and carboxy terminals were rotated. C57BL/10 mice were immunized with 100 micrograms of peptide in complete Freund's adjuvant (FA) on day 0, followed by an immunization with peptide (100 micrograms) in complete FA on day 14. By day 21 the immunodominant epitope in both chimeras as measured by ELISA was the one located at the carboxy terminus. A pepscan of the VD 1-4 antisera revealed a main peak in VD 4 which had been previously identified by neutralizing MAbs. The VD 4-1 antisera gave a peak in the VD 1 region which did not correspond to regions previously mapped with neutralizing MAbs. The VD 1-4 antisera but not the VD 4-1 antisera was able to neutralize in vitro serovar E. In summary, the position of these chlamydial epitopes within a chimeric peptide greatly influenced the resulting immune response.

[Content determination of baicalin by ultraviolet second order derivative spectra]

By the method of UV second order derivative spectra, baicalin in contents in the Lanqin Oral Liquid were determined. Able to eliminate the influence of other constituents, this method is simple, rapid, sensitive and accurate.

Reversal of in vitro lipopolysaccharide-induced suppression of contraction in rat aorta by NG-nitro-arginine, diphenyleneiodonium and di-2-thienyliodonium

The effects of NG-nitro-L-arginine (L-NNA), D-NNA, diphenyleneiodonium and di-2-thienyliodonium on contraction were studied in endothelium-denuded rat aortic rings incubated for 4 h with lipopolysaccharide (10 mu g ml-1) or vehicle. Lipopolysaccharide reduced Emax and increased EC50 of the phenylephrine (10-9-10-5 M) curve. Addition of D-NNA (4, 6 x 10-4 M), L-NNA (1, 10 x 10-6 M) and diphenyleneiodonium (1, 3 x 10-7 M), but not di-2-thienyliodonium (10-7 M), increased Emax and reduced EC50 of the phenylephrine curve of lipopolysaccharide-incubated but not control rings. Therefore, D-NNA, L-NNA and diphenyleneiodonium, but not di-2-thienyliodonium, inhibit inducible NO synthase in vascular smooth muscles.

Binding specificity of post-activated neocarzinostatin chromophore drug-bulged DNA complex studied using electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) was employed to characterize the binding specificity of a bulged 22-mer DNA hairpin with a post-activated neocarzinostatin chromophore (NCS-Chrom) having two similar forms, where 2a has an H in a location for which 2b has it replaced by a CH2OH group. Specific binding of 2a to the bulged 22-mer DNA was observed whereas little binding was detected for 2a to non-bulged DNA 19-mer and 12-mer duplexes. The stoichiometry of the 22-mer DNA complex with 2a was determined to be predominantly 1:1. Substitution of hydrogen in 2a for the hydroxymethylene group in 2b dramatically reduced the binding strength to the 22-mer DNA. Little complex formation was observed for 2b and 22-mer DNA based upon the ESI-MS data, consistent with earlier fluorescence studies. The results indicate that ESI-MS can be a sensitive technique for probing conformational specificity in studies of biomolecular binding.

Insertion element IS1296 in Mycoplasma mycoides subsp. mycoides small colony identifies a European clonal line distinct from African and Australian strains

Strains of Mycoplasma mycoides subsp. mycoides small colony (SC) type, the agent of contagious bovine pleuropneumonia (CBPP), were analysed with respect to the polymorphism of distribution of a newly discovered insertion element, IS1296, on the chromosome. Analysis of 64 strains isolated from Europe, Africa and Australia, including four vaccine strains and the type strain PG1, revealed ten different IS patterns, forming two main clusters. The European strains originated from outbreaks of CBPP in different countries, and from various other sources such as semen and preputial washings from cattle, lungs from goats and buffalo, and milk from sheep. They showed identical IS1296 patterns, except one strain which had an additional IS1296 element, but the pattern belonged to the same cluster. This shows that the strains from Europe form a clonal lineage. The strains originating from different geographical parts of the African continent and from Australia showed four closely related IS1296 patterns which belong to a separate cluster. This indicates that strains from Africa and Australia form a clonal lineage different from that of the European strains, suggesting that the sporadic cases of CBPP that have re-emerged in Europe almost 15 years after the last declared endemic case in 1967 arose from an established reservoir within Europe rather than being the result of repeated importation from Africa and Australia. While most strains from Africa and Australia had the same IS1296 pattern, all vaccine strains could be distinguished by an individual pattern. The type strain PG1 also had a particular IS1296 pattern which belongs to the cluster of the strains from Africa and Australia. The molecular definition of clonality of M. mycoides subsp. mycoides SC strains with IS1296 represents a rapid and reproducible method for subtyping and differentiation of vaccine strains. It permits at the present time the definition of two main clonal lines, one including the strains from the European continent and a second with strains from Africa and Australia.

Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes

Previous X-ray crystallographic studies have revealed that the catalytic domain of a DNA methyltransferase (Mtase) generating C5-methylcytosine bears a striking structural similarity to that of a Mtase generating N6-methyladenine. Guided by this common structure, we performed a multiple sequence alignment of 42 amino-Mtases (N6-adenine and N4-cytosine). This comparison revealed nine conserved motifs, corresponding to the motifs I to VIII and X previously defined in C5-cytosine Mtases. The amino and C5-cytosine Mtases thus appear to be more closely related than has been appreciated. The amino Mtases could be divided into three groups, based on the sequential order of motifs, and this variation in order may explain why only two motifs were previously recognized in the amino Mtases. The Mtases grouped in this way show several other group-specific properties, including differences in amino acid sequence, molecular mass and DNA sequence specificity. Surprisingly, the N4-cytosine and N6-adenine Mtases do not form separate groups. These results have implications for the catalytic mechanisms, evolution and diversification of this family of enzymes. Furthermore, a comparative analysis of the S-adenosyl-L-methionine and adenine/cytosine binding pockets suggests that, structurally and functionally, they are remarkably similar to one another.

[The cloning and expression of human secreted interleukin 2 receptor alpha chain gene in eukaryotic cells]

By deleting the sequences encoding the cytoplasmic domain, transmembrane domain and the 5' untranslated region, human interleukin-2 receptor alpha cDNA fragment was subcloned into an eukaryotic expression vector pRc/CMV. The recombinant plasmid was then transfected into CHO cells by either electroporation or calcium phosphate precipitation. 11 G418-resistent clones were randomly selected for detection of mRNA expression. 5 clones out of the 11 were proved to be positively hybridyzed with IL-2R alpha cDNA probe. All of the 5 positive cell lines also expressed sIL-2R alpha in their supernatants as detected by ELISA. The establishment of rhsIL-2R alpha cell lines is of importance in the detection and purification of IL-2 based on the ability of affinity binding between IL-2 and its recombinant receptor.

Photoperiodic exposure and time of day modulate the expression of arginine vasopressin mRNA and vasoactive intestinal peptide mRNA in the suprachiasmatic nuclei of Siberian hamsters

In hamsters, changes in ambient photoperiod lead to alterations in the circadian rhythm of pineal melatonin secretion and subsequent changes in reproductive function. The present study examined whether photoperiod also alters 24-h rhythms in neuropeptide mRNA levels in the SCN of Siberian hamsters. In situ hybridization and quantitative autoradiography were used to assess messenger RNA levels for vasopressin (AVP) and vasoactive intestinal peptide (VIP) in the SCN of hamsters sacrificed at six times of day following exposure to long (16 h light/day) or short (10 h light/day) photoperiod for 2 weeks. Both AVP mRNA and VIP mRNA in the SCN were significantly affected by time of day and photoperiodic exposure. The 24-h profiles of AVP mRNA and VIP mRNA showed different relationships to the light: dark cycle, suggesting that these profiles are differentially regulated. In general, short photoperiod tended to suppress AVP mRNA and VIP mRNA in the SCN; this effect on AVP mRNA was significant at two times of day. These results complement and extend previous findings of 24-h h profiles in neuropeptide mRNA expression in the rat SCN by showing that these 24-h profiles are also characteristic of the Siberian hamster SCN and that they can be modulated by photoperiod.

Probing the mechanism of CRP activation by site-directed mutagenesis: the role of serine 128 in the allosteric pathway of cAMP receptor protein activation

Upon activation by cAMP, Escherichia coli cAMP receptor protein (CRP) controls the expression of a network of catabolite sensitive genes. The activation of CRP by cAMP involves conformational changes such as realignments between subunits and domains within the protein. To understand the molecular events that lead to the activation of CRP, point mutations at position 128 were introduced via site-directed mutagenesis in an attempt to specifically affect the subunit interfacial interactions, as well as the ligand-binding reaction. The biochemical and biophysical properties of these mutants were rigorously tested with the goal of identifying the partial reactions in the activation pathway that are perturbed by this specific mutation. Results from this study suggest that mutation of Ser 128 to Ala or Pro does not significantly disturb the overall secondary structure as monitored by circular dichroism. The energetics of subunit-subunit interaction and protein stability were monitored by sedimentation and spectroscopic techniques. Although these mutants were designed to interrupt intersubunit interactions, the energetics of subunit association and protein stability remain quantitatively the same as those of the wild-type CRP. Nevertheless, the ability of the subunit to be realigned to the DNA-binding form is significantly affected as reflected by the pronounced decrease in the susceptibility of mutant CRP to proteolytic digestion in the presence of cAMP. In addition, the binding affinity of cAMP to the first ligand site in mutants S128A and S128P is the same as that of the wild type, but the affinity to the second ligand site is reduced. This observation indicates that mutation at position 128 affects ligand binding by amplifying the magnitude of negative cooperativity. Mutation at residue 128 does not impair the ability of interdomain interactions as indicated by the quantitative response of a spectroscopic probe in the DNA-binding domain to the binding of cAMP to the ligand-binding domain. The S128A mutant binds to a specific DNA sequence about 50-fold weaker than the wild-type CRP, while the mutant S128P has no measurable DNA affinity under the same conditions. This observation is consistent with the in vivo result that both mutants display an inactive CRP phenotype (CRP-). In summary, these results suggest that communication between domains induced by cAMP binding can be dissociated from the proper subunit realignment of the CRP dimer that is crucial for the activation of CRP.(ABSTRACT TRUNCATED AT 400 WORDS)

Characterization of cytochrome c variants with high-resolution FTICR mass spectrometry: correlation of fragmentation and structure

The dissociation of cytochrome c ions (15+ charge state) generated by electrospray ionization has been studied by Fourier transform ion cyclotron resonance mass spectrometry (FTICR) using a sustained off-resonance irradiation/collision-induced dissociation (SORI-CID) technique. Over 95% of the fragment ions can be accurately assigned (to better than 10 ppm), yielding information on the primary sequences of the various proteins. Up to four stages of mass spectrometry (MS4) have been achieved without the need for quadrupole excitation/collisional cooling of the product ions. The subtle structural differences among the cytochrome c variants (from bovine, tuna, rabbit, and horse) are clearly reflected in their fragmentation patterns: replacing 3 out of 104 residues of the cytochrome c is shown to dramatically change the dissociation pattern. Of particular importance are a variety of results indicating that the dissociation of the cytochrome c's is influenced by higher-order structure and charge location, in addition to the primary structure (i.e., sequence). No fragmentation is observed in the region between residues 10-20 and little dissociation between residues 70-90. This is most likely due to the interactions of the heme group with the polypeptide chain, and such a heme "footprinting" pattern is analogous to the protein conformation in solution. These studies demonstrate that electrospray ionization-FTICR using SORI-CID can be a useful tool to probe not only the small differences in the primary sequences of proteins but also suggest the potential for probing their higher-order structures and yielding information not readily available from H/D exchange or circular dichoism studies.

Metabolism of 1,3-butadiene to butadiene monoxide in mouse and human bone marrow cells

1,3-Butadiene (BD), a gas used in the production of rubber and plastics, induces a high incidence of leukemias and lymphomas in B6C3F1 mice. Because of the potential involvement of the hematopoietic system in response to BD, we have examined metabolism of BD by B6C3F1 mouse and human bone marrow and by purified human myeloperoxidase (MPO), an enzyme rich in bone marrow. BD was metabolized to butadiene monoxide (BMO) by MPO and by mouse and human bone marrow cells. In all of these systems metabolism was stimulated by hydrogen peroxide suggesting a peroxidase-mediated process. In B6C3F1 mouse bone marrow cell lysates, hydrogen peroxide but not NADPH stimulated metabolism suggesting that cytochrome P450 was not involved in BMO formation. Metabolism of BD to BMO in hydrogen peroxide-fortified mouse bone marrow cell lysates was more than two orders of magnitude lower than in either NADPH-fortified rat or mouse hepatic microsomes. Experiments using both mouse and human bone marrow cells showed that cells from both sources could generate BMO from BD. These data show that BD can be converted to BMO in a target organ of BD carcinogenicity.

Identification and characterization of IS1296 in Mycoplasma mycoides subsp. mycoides SC and presence in related mycoplasmas

IS1296, a new insertion sequence belonging to the IS3 family of insertion elements has been identified in Mycoplasma mycoides subsp. mycoides (Mmm) biotype small colony (SC), the agent of contagious bovine pleuropneumonia (CBPP). IS1296 is 1485-bp long and has 30-bp inverted repeats. It contains two open reading frames, ORFA and ORFB, which show significant similarities to the ORFs which encode the transposase function of IS elements of the IS3 family, in particular IS150 of Escherichia coli. IS1296 is present in 19 copies in Mmm SC-type strain PG1 and in 18 copies in a recently isolated field strain L2. It seems to transpose at low frequency in Mmm SC. IS1296 is also present in 5 copies in Mmm biotype large colony (LC)-type strain Y-goat, and in two copies in Mycoplasma sp. 'bovine group 7' reference strain PG50. It is, however, not present in other species of the 'mycoides cluster' or other closely related Mycoplasma sp. of ruminants.

Structure and function of DNA methyltransferases

In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. Structural work on HhaI DNA methyltransferase demonstrates that the substrate nucleotide is completely flipped out of the helix during the modification reaction and has provided much insight into the enzymatic properties of S-adenosyl-L-methionine (SAM)-dependent DNA-modifying enzymes. Structural comparison of three enzymes, HhaI C5-cytosine methyltransferase, TaqI N6-adenine methyltransferase, and catechol O-methyltransferase, reveals a striking similarity in protein folding and indicates that many SAM-dependent methyltransferases have a common catalytic-domain structure. This feature permits the prediction of tertiary structure for other DNA, RNA, protein, and small-molecule methyltransferases from their amino acid sequences, including the eukaryotic CpG methyltransferases.

Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases

M.HhaI, M.TaqI and COMT are DNA methyltransferases (MTases) which catalyze the transfer of a methyl group from the cofactor AdoMet to C5 of cytosine, to N6 of adenine and to a hydroxyl group of catechol, respectively. The larger catalytic domains of the bilobal proteins, M.HhaI and M.TaqI, and the entire single domain of COMT have an alpha/beta structure containing a mixed central beta-sheet. These domains have very similar folding. By allowing appropriate 'insertions' or 'deletions' in the backbones of the three structures, it was possible to find more conserved motifs in M.TaqI and COMT. The similarity in protein folding and the equivalence of amino-acid sequences revealed by the structural alignment indicate that many AdoMet-dependent MTases may share a common catalytic domain structure.

Crystal structure of the PvuII restriction endonuclease

Crystal structures have now been determined for the R.PvuII restriction endonuclease as a protein-DNA complex [Cheng et al., EMBO J. 13 (1994) 3927-3935; this report] and in apo-form [Athanasiadis et al., Nature Struc. Biol. 1 (1994) 469-475; our unpublished result]. The structures indicate how the interaction with DNA might proceed [Riddihough, Nature 370 (1994) 78].

Regulation of DNA replication in irradiated cells by trans-acting factors

We compared DNA replication activity in cytoplasmic extracts prepared from irradiated and nonirradiated HeLa cells using a simian virus 40 (SV40)-based in vitro replication assay. The assay measures semi-conservative DNA replication in a plasmid carrying the SV40 origin of replication and requires SV40 T antigen as the sole noncellular protein. The plasmid DNA used in the replication reaction is never exposed to radiation. We find that replication of plasmid DNA is significantly reduced when cytoplasmic extracts from irradiated cells are used. Since plasmid replication proceeds to completion in extracts from irradiated cells, the observed reduction in the over-all replication activity is probably due to a reduction in the efficiency of initiation events. The degree of inhibition of DNA replication after exposure to 10, 30 and 50 Gy X rays as measured in vitro using this assay is similar to that measured in intact cells immediately before processing for extract preparation. These observations are compatible with the induction or activation by ionizing radiation of a factor(s) that inhibits in trans DNA replication. The results contribute to our understanding of the mechanism(s) developed by the cells to regulate DNA replication when exposed to clastogenic agents. Such processes may be of significance in the restoration of DNA integrity, and may define yet another checkpoint operating during S at the level of clusters of replicons.

Universal catalytic domain structure of AdoMet-dependent methyltransferases

The DNA methyltransferases, M.HhaI and M.TaqI, and catechol O-methyl-transferase (COMT) catalyze the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to carbon-5 of cytosine, to nitrogen-6 of adenine, and to a hydroxyl group of catechol, respectively. The catalytic domains of the bilobal proteins, M.HhaI and M.TaqI, and the entire single domain of COMT have similar folding with an alpha/beta structure containing a mixed central beta-sheet. The functional residues are located in equivalent regions at the carboxyl ends of the parallel beta-strands. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-dependent methyltransferases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-dependent methyltransferases from their amino acid sequences.

Effect of ionizing radiation on the expression of chloramphenicol acetyltransferase gene under the control of commonly used constitutive or inducible promoters

We examined the effect of ionizing radiation on the expression of the chloramphenicol acetyltransferase (CAT) gene driven by commonly used viral or semi-synthetic promoters in transient transfection assays using COS-7 cells. Specifically, we studied the constitutive early promoters of cytomegalovirus (CMV), Rous sarcoma virus (RSV), and the simian virus 40 (SV40), and the inducible promoters from mouse mammary tumour virus (MMTV, inducible by dexamethasone) and the semi-synthetic SVlacO promoter (SVlacO, inducible by isopropyl beta-D-thiogalactoside). CAT activity was measured in cells exposed to 20 Gy X-rays and in non-irradiated controls 46 h after transient transfection. We observed that CAT expression from the CMV and SV40 promoters remained unchanged in cells exposed to radiation. Similar results were obtained with MMTV and SVlacO promoters when cells were irradiated 16 h after induction. However, expression from the RSV promoter was significantly increased after radiation exposure and similar results were obtained with the MMTV and SVlacO promoters when irradiation immediately preceded induction. The results suggest a classification of promoters as radiation-independent and -dependent. The constitutive CMV and SV40 promoters belong to the first category, whereas RSV belongs to the second category. The inducible MMTV and SVlacO promoters would be classified to the first category when induction precedes irradiation by 16 h, and to the second category when irradiation immediately follows induction. It will be desirable to use promoters under conditions that classify them to the first category to study the effect on cellular response to radiation of genes suspected to influence the intrinsic radiosensitivity of cells.

Interface for a four-sector mass spectrometer with a dual-purpose collision cell: High transmission at low to intermediate energies

A new interface system that consists of an ion decelerator, a floating collision cell-chemical ionization ion source, and an ion extractor was designed and installed in the third field-free region of a four-sector tandem mass spectrometer. Important features include the use of cylindrical deceleration lenses and an extraction lens assembly. This new design was found to provide enhancement of ion transmission at low to intermediate ion kinetic energies (3 eV to 1 keV) compared with the standard collision cell design. Collision-induced dissociation experiments from 3 eV to 10 keV and ion-molecule reactions of mass-selected ions can be performed conveniently. A second, grounded, collision cell is located after the extraction lenses, which allows MS(4) experiments to be carried out via the normal linked (B/E) scan function in MS2. Incorporation of chemical ionization capability into the electrically isolated collision cell makes it possible to carry out neutralization chemical-reionization mass spectrometry.

Crystal structure of casein kinase-1, a phosphate-directed protein kinase

The structure of a truncated variant of casein kinase-1 from Schizosaccharomyces pombe, has been determined in complex with MgATP at 2.0 A resolution. The model resembles the 'closed', ATP-bound conformations of the cyclin-dependent kinase 2 and the cAMP-dependent protein kinase, with clear differences in the structure of surface loops that impart unique features to casein kinase-1. The structure is of unphosphorylated, active conformation of casein kinase-1 and the peptide-binding site is fully accessible to substrate.

DNA modification by methyltransferases

Enzymatic methylation of DNA plays important roles in both prokaryotes and eukaryotes. Structural study of the HhaI DNA methyltransferase has provided considerable insight into the chemistry of C5-cytosine methylation. The DNA-protein complex reveals a substrate cytosine flipped out of the double helix during the reaction, and a novel two-loop DNA-binding motif used for both sequence recognition and flipping the base. Structural comparison of HhaI C5-cytosine methyltransferase, TaqI N6-adenine methyltransferase, and catechol O-methyltransferase reveals a common catalytic domain structure, which might be universal among S-adenosyl-L-methionine (SAM)-dependent methyltransferases.

[Isolation and identification of enteric adenovirus in China]

Enteric adenovirus type 40/41 is considered to be the second major cause of gastroenteritis in young children. In this study fecal specimens 86-123 from diarrhea patients were isolated and examined in Grahm 293 cells. This induced cytopathic effect (CPE) at this cells. Viral particles were also found in fecal specimens and by electron microscopy. Examination of the isolate with Cambridge Biotech Adenoclone-Type 40/41 test kit indicated that it contained EAd. On the basis of the above studies, one strain of EAd was the first isolated virus in China.

Ossification processes and perichondral ossification groove of Ranvier: a morphological study in developing human calcaneus and talus

In this histologic-radiologic investigation of 32 feet of 16 fetuses and newborns ranging in age from 15 to 44 weeks, two types of ossification, i.e., endochondral ossification through primary ossification center and intramembraneous ossification through periosteal bone formation (PBF), were found to coexist in both calcaneus and talus. In addition, Ranvier's grooves (RG), or perichondral ossification groove, also was observed as a shallow, saucer-like or semicircular structure. As with PBFs, there are three and two RGs in the calcaneus and talus, respectively. RG and PBF appeared in time order and were located regularly in the concave areas of the adult calcaneus and talus. The findings support the hypothesis that one function of PBF and RG is to limit the growth of the calcaneus and talus. Thus, they are responsible for the irregular contour of the calcaneus and talus.

Bio-affinity characterization mass spectrometry

A new approach, bio-affinity characterization mass spectrometry (BACMS), aimed at providing a more rapid, sensitive and potentially more flexible alternative to techniques presently employed for the characterization of noncovalent interactions in mixtures, such as would be encountered in combinatorial chemistry, in presented. BACMS avoids some of the difficulties and potential artifacts associated with affinity chromatography since the noncovalent associations occur in solution; thus, BACMS avoids the requirement of solid support media and the development of non-interfering linker species. This paper describes the conceptual basis for the methodology and its potential use in applications which include the screening of high affinity ligands in support of new drug development. BACMS exploits new Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry technologies which, when coupled to electrospray ionization (ESI), allow the investigation of specific noncovalent complexes formed in solution. BACMS utilizes the well-known attributes of FTICR, such as the high resolution mass analysis and (MS)n (n > or = 2) capabilities; however, it is even more directly a result of recently developed techniques involving quadrupolar excitation, such as selected-ion accumulation. These tools are demonstrated and the results illustrate the extraordinary sensitivity achievable (solution concentration of 1 x 10-9 M without the use of separations prior to ESI). Thus, the new capabilities demonstrated here, in conjunction with ESI, will be useful for the investigation of very low relative concentration noncovalent association directly from solution, and promote a faster alternative for combinatorial mixture screening and analysis.

Vascular pharmacology of methylene blue in vitro and in vivo: a comparison with NG-nitro-L-arginine and diphenyleneiodonium

1. The vascular effects of the soluble guanylyl cyclase inhibitor, methylene blue as well as the nitric oxide (NO) synthase inhibitors, NG-nitro-L-arginine (L-NOARG) and diphenyleneiodonium (DPI) were studied in rat isolated aortic rings and conscious, unrestrained rats. 2. Acetylcholine (ACh) and sodium nitroprusside (SNP) caused concentration-dependent relaxation of preconstricted aortic rings. Both methylene blue (1 x 10(-5) M) and L-NOARG (3 x 10(-5) M) abolished ACh-induced relaxation; however, methylene blue but not L-NOARG shifted the concentration-response curve of SNP to the right. 3. In conscious rats, i.v. infusion of methylene blue (1.1 x 10(-5) mol kg-1 min-1), at a concentration which reduced the aortic tissue level of cyclic GMP by 50%, did not significantly alter mean arterial pressure (MAP) and heart rate (HR). In contrast, i.v. bolus injection of L-NOARG (1.5 x 10(-4) mol kg-1) markedly increased MAP and decreased HR. 4. Both ACh and SNP dose-dependently decreased MAP in conscious rats. Methylene blue did not alter the magnitude or duration of ACh- or SNP-induced depressor responses. L-NOARG, on the other hand, significantly though incompletely, reduced the magnitude and duration of the depressor response to ACh but not SNP. The depressor response to ACh or SNP was not altered by pretreatment with indomethacin (1.4 x 10(-5) mol kg-1) or capsaicin (3.3 x 10(-4) mol kg-1). 5. NG-nitro-L-arginine methyl ester (L-NAME) also caused dose-dependent increases in MAP in conscious rats. Both methylene blue and DPI (1 x 10-5 mol kg-1) selectively shifted the dose-pressor response curve of L-NAME to the right.6. These results suggest that: (1) the inhibition of endogenous NO biosynthesis does not necessarily lead to pressor response in vivo, (2) L-NOARG may not produce pressor response solely via the inhibition of endogenous endothelial NO biosynthesis, and (3) the depressor responses to ACh and SNP may not involve the release of NO or prostanoids or afferent nerve transmitters.

Absolute requirement of cyclic nucleotide in the activation of the G141Q mutant cAMP receptor protein from Escherichia coli

cAMP receptor protein (CRP), when interacting with cAMP, controls the expression of a network of catabolite-sensitive genes in Escherichia coli. To understand the molecular events that lead to the activation of CRP, a combined approach of site-directed mutagenesis and thermodynamic analysis was employed to study a member of a specific class of CRP mutant, CRP, which activates the in vivo expression of CRP-dependent operons in cya- strains in the absence of exogenous cAMP. Results from in vitro studies show that the CRP mutant G141Q absolutely requires cAMP for interacting with specific DNA. A quantitative comparison of the thermodynamic parameters governing ligand binding and DNA-protein complex formation in the presence of different cyclic nucleotides leads to the conclusion that this CRP mutant is activated only in the presence of cyclic nucleotides. The specificity toward cyclic nucleotides exhibited by wild-type CRP is lost in this mutant. Furthermore, the binding affinity of the ligand for the first binding site of the mutant is essentially the same as that of wild-type CRP regardless of the identity of the cyclic nucleotide. Hence, the observed in vivo activation of CRP-dependent operons by G141Q in the absence of exogenous cAMP is most likely the consequence of the replacement of cAMP by other cyclic nucleotides to activate the mutant. It is also possible that trace levels of cAMP present in the cya- strain could account for the in vivo activation of the mutant. Furthermore, these results indicate that this CRP mutant does not assume the activated conformation in the absence of cyclic nucleotides, in contrast to the current model derived from results of in vivo studies.

Effects of liuwei dihuang wan [symbol: see text:bd and some other TCM drugs on bone biomechanics and serum 25 (OH)D3 content in rats

After a relatively long-term injection of hydrocortisone into rats, the strength of bone (anti-stress capacity) reduced evidently, while the rigidity (anti-deformity capacity) increased markedly (ie, bone fragility elevated). At the same time, the content of serum 25(OH)D3 decreased remarkably. After oral administration of Liuwei Dihuang Wan ([see symbol: see text]), anti-stress capability of bone increased evidently and its anti-deformity capability returned to normal; however, there was no elevation of serum 25(OH)D3 content. The effect of Longmu Zhuanggu Chongji ([see symbol: see text]) or Jisheng Shenqi Wan (see symbol: see text]) was lower than that of Liuwei Dihuang Wan. The experiments suggests that Liuwei Dihuang Wan is beneficial to preventing and curing osteoporosis, but no correlation between its mechanism and the metabolism of 25(OH)D3 was demonstrated.